JAL-2371 skip upper-casing consensus as it already is

[jalview.git] / src / jalview / schemes / PIDColourScheme.java

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index a6301fa..657d6b0 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -31,16 +31,15 @@ import java.util.Map;
 
 public class PIDColourScheme extends ResidueColourScheme
 {
-  public Color[] pidColours;
+  private static final Color[] pidColours = { new Color(100, 100, 255),
+      new Color(153, 153, 255), new Color(204, 204, 255), };
 
-  public float[] thresholds;
+  private static final float[] thresholds = { 80, 60, 40, };
 
   SequenceGroup group;
 
   public PIDColourScheme()
   {
-    this.pidColours = ResidueProperties.pidColours;
-    this.thresholds = ResidueProperties.pidThresholds;
   }
 
   @Override
@@ -48,16 +47,15 @@ public class PIDColourScheme extends ResidueColourScheme
           String consensusResidue, float pid)
   {
     /*
-     * make everything uppercase; note this does nothing (fast)
-     * if consensusResidue is already uppercase
+     * compare as upper case; note consensusResidue is 
+     * always computed as uppercase
      */
-    consensusResidue = consensusResidue.toUpperCase();
     if ('a' <= c && c <= 'z')
     {
       c -= ('a' - 'A');
     }
 
-    if (consensusResidue == null)
+    if (consensusResidue == null || Comparison.isGap(c))
     {
       return Color.white;
     }
@@ -71,15 +69,12 @@ public class PIDColourScheme extends ResidueColourScheme
             String.valueOf(c));
     if (matchesConsensus)
     {
-      if (!Comparison.isGap(c))
+      for (int i = 0; i < thresholds.length; i++)
       {
-        for (int i = 0; i < thresholds.length; i++)
+        if (pid > thresholds[i])
         {
-          if (pid > thresholds[i])
-          {
-            colour = pidColours[i];
-            break;
-          }
+          colour = pidColours[i];
+          break;
         }
       }
     }